Error running test files

[koushik1989]

Dear Developers, thank you for developing a wonderful tool like PoseiDon. I installed nextflow version 20.04.1.5335 and docker 20.10.10 and followed every step mentioned in github. But when I run the following test run I get an error.

$ nextflow run hoelzer/poseidon -r v1.0.1 -profile local,docker --fasta ~/.nextflow/assets/hoelzer/poseidon/test_data/bats_mx1_small.fasta N E X T F L O W ~ version 20.12.0-edge Launching hoelzer/poseidon [goofy_liskov] - revision: 4f23bb667f [v1.0.1] WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE

P O S E I D O N

Profile: local,docker

Current User: fly-lab Nextflow-version: 20.12.0-edge Starting time: 12-12-2020 09:14 UTC Workdir location: /tmp/nextflow-work-fly-lab

CPUs to use per process: 6, maximal CPUs to use: 4

Tree root species: NA Reference species: NA

Use KH-insignificant breakpoints: no

executor > local (1) [dd/1d80b5] process > check_fasta_format (1) [ 0%] 0 of 1 [- ] process > translatorx - [- ] process > check_aln - [- ] process > remove_gaps - [- ] process > raxml_nt - [- ] process > raxml_aa - [- ] process > raxml2drawing - [- ] process > nw_display - [- ] process > barefoot - [- ] process > model_selection - [- ] process > gard_detect - [- ] process > gard_process - [- ] process > codeml_built - [- ] process > codeml_run - [- ] process > codeml_combine - [- ] process > tex_built - [- ] process > pdflatex_single - [- ] process > build_fragments - [- ] process > frag_raxml_nt - [- ] process > frag_raxml_aa - [- ] process > frag_raxml2drawing - [- ] process > frag_nw_display - [- ] process > frag_barefoot - [- ] process > frag_codeml_built - executor > local (1) [dd/1d80b5] process > check_fasta_format (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > translatorx - [- ] process > check_aln - [- ] process > remove_gaps - [- ] process > raxml_nt - [- ] process > raxml_aa - [- ] process > raxml2drawing - [- ] process > nw_display - [- ] process > barefoot - [- ] process > model_selection - [- ] process > gard_detect - [- ] process > gard_process - [- ] process > codeml_built - [- ] process > codeml_run - [- ] process > codeml_combine - [- ] process > tex_built - [- ] process > pdflatex_single - [- ] process > build_fragments - [- ] process > frag_raxml_nt - [- ] process > frag_raxml_aa - [- ] process > frag_raxml2drawing - [- ] process > frag_nw_display - [- ] process > frag_barefoot - [- ] process > frag_codeml_built - [- ] process > frag_codeml_run - [- ] process > frag_codeml_combine - [- ] process > frag_tex_built - [- ] process > frag_pdflatex_single - [- ] process > tex_combine - [- ] process > pdflatex_full - [- ] process > frag_aln_html - [- ] process > html_frag - [- ] process > frag_publish - [- ] process > frag_html_codeml - [- ] process > html - [- ] process > html_codeml - [- ] process > html_params - [- ] process > html_recomb - Error executing process > 'check_fasta_format (1)'

Caused by: Process check_fasta_format (1) terminated with an error exit status (126)

Command executed:

fasta_format_checker.rb bats_mx1_small.fasta bats_mx1_small.checked.fasta bats_mx1_small.log bats_mx1_small_internal2input_species.tsv bats_mx1_small_input2internal_species.tsv NA NA

replace newlines with 'foobar' to replace this again in the nextflow for better terminal output

LOG=$(sed -z 's/\n/foobar/g' bats_mx1_small.log)

Command exit status: 126

Command output: (empty)

Command error: docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Frun%2Fdocker.sock/v1.24/containers/create?name=nxf-Aq2yz0pzT8039End0fK0PHYw": dial unix /var/run/docker.sock: connect: permission denied. See 'docker run --help'.

Work dir: /tmp/nextflow-work-fly-lab/dd/1d80b54011f8c12626687a7eb28915

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

Kindly help me out as PoseiDon is the only hope for a biologist like me with no much coding knowledge.

[koushik1989]

Dear developers, I have successfully resolved the issue. The problem was with Docker.

Thanks.

[hoelzer]

Great, thanks for your interest into the tool!